Research workbench
Crystal structure of human methionine aminopeptidase-2 in complex with an inhibitor GSK1978537A (compound 27)
Analyse Crystal structure of human methionine aminopeptidase-2 in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A13
- Type
- protein
- Length
- 366 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine aminopeptidase 2
- EC
- 3.4.11.18
- UniProt
- P50579
- Ligands
- QW5, MN, PO4
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine aminopeptidase 2 (EC 3.4.11.18) | protein | 366 | 32% helix, 25% strand | P50579 |
Ligands and binding sites
- QW5 · 5-chloranyl-3-(3-methoxyphenyl)-1~{H}-indole-2-carboxamide · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.68 | 0.84 | 40 | PO4, QW5 |
| 2 | 61 | 0.32 | 0.76 | 18 | empty |
| 3 | 65 | 0.29 | 0.73 | 12 | PO4 |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7A13 · Crystal structure of human methionine aminopeptidase-2 in complex with an inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P50579 · AlphaFold monomer V2.0 prediction for methionine aminopeptidase 2 (P50579) · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P50579
- Elsewhere: RCSB PDB 7A13 · PDBe 7A13 · UniProt P50579
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